Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 19 15:38:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo0_36451/08_2023/8jo0_36451_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo0_36451/08_2023/8jo0_36451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo0_36451/08_2023/8jo0_36451.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo0_36451/08_2023/8jo0_36451.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo0_36451/08_2023/8jo0_36451_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo0_36451/08_2023/8jo0_36451_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 21 5.49 5 Mg 7 5.21 5 S 199 5.16 5 C 17375 2.51 5 N 4579 2.21 5 O 5181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 4": "OE1" <-> "OE2" Residue "H GLU 38": "OE1" <-> "OE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "I GLU 4": "OE1" <-> "OE2" Residue "I GLU 38": "OE1" <-> "OE2" Residue "I GLU 88": "OE1" <-> "OE2" Residue "J GLU 4": "OE1" <-> "OE2" Residue "J GLU 38": "OE1" <-> "OE2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J GLU 97": "OE1" <-> "OE2" Residue "K GLU 4": "OE1" <-> "OE2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K GLU 88": "OE1" <-> "OE2" Residue "L GLU 4": "OE1" <-> "OE2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L GLU 88": "OE1" <-> "OE2" Residue "M GLU 4": "OE1" <-> "OE2" Residue "M GLU 38": "OE1" <-> "OE2" Residue "M GLU 88": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B ARG 436": "NH1" <-> "NH2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "C ASP 145": "OD1" <-> "OD2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C GLU 263": "OE1" <-> "OE2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C GLU 364": "OE1" <-> "OE2" Residue "C GLU 383": "OE1" <-> "OE2" Residue "C ARG 436": "NH1" <-> "NH2" Residue "C ARG 440": "NH1" <-> "NH2" Residue "C ARG 448": "NH1" <-> "NH2" Residue "C ARG 483": "NH1" <-> "NH2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D GLU 263": "OE1" <-> "OE2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D GLU 424": "OE1" <-> "OE2" Residue "D ARG 436": "NH1" <-> "NH2" Residue "D ARG 440": "NH1" <-> "NH2" Residue "D ARG 448": "NH1" <-> "NH2" Residue "D GLU 481": "OE1" <-> "OE2" Residue "D ARG 483": "NH1" <-> "NH2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E GLU 256": "OE1" <-> "OE2" Residue "E GLU 263": "OE1" <-> "OE2" Residue "E GLU 289": "OE1" <-> "OE2" Residue "E GLU 315": "OE1" <-> "OE2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E GLU 324": "OE1" <-> "OE2" Residue "E GLU 341": "OE1" <-> "OE2" Residue "E GLU 364": "OE1" <-> "OE2" Residue "E GLU 383": "OE1" <-> "OE2" Residue "E GLU 424": "OE1" <-> "OE2" Residue "E ARG 436": "NH1" <-> "NH2" Residue "E ARG 440": "NH1" <-> "NH2" Residue "E ARG 448": "NH1" <-> "NH2" Residue "E ARG 483": "NH1" <-> "NH2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "F GLU 255": "OE1" <-> "OE2" Residue "F GLU 256": "OE1" <-> "OE2" Residue "F GLU 263": "OE1" <-> "OE2" Residue "F GLU 289": "OE1" <-> "OE2" Residue "F GLU 316": "OE1" <-> "OE2" Residue "F GLU 324": "OE1" <-> "OE2" Residue "F GLU 341": "OE1" <-> "OE2" Residue "F GLU 364": "OE1" <-> "OE2" Residue "F GLU 383": "OE1" <-> "OE2" Residue "F ARG 436": "NH1" <-> "NH2" Residue "F ARG 440": "NH1" <-> "NH2" Residue "F ARG 448": "NH1" <-> "NH2" Residue "F ARG 483": "NH1" <-> "NH2" Residue "F GLU 486": "OE1" <-> "OE2" Residue "F GLU 527": "OE1" <-> "OE2" Residue "G GLU 255": "OE1" <-> "OE2" Residue "G GLU 263": "OE1" <-> "OE2" Residue "G GLU 289": "OE1" <-> "OE2" Residue "G GLU 324": "OE1" <-> "OE2" Residue "G GLU 341": "OE1" <-> "OE2" Residue "G GLU 364": "OE1" <-> "OE2" Residue "G GLU 383": "OE1" <-> "OE2" Residue "G ARG 436": "NH1" <-> "NH2" Residue "G ARG 440": "NH1" <-> "NH2" Residue "G ARG 448": "NH1" <-> "NH2" Residue "G ARG 483": "NH1" <-> "NH2" Residue "G GLU 486": "OE1" <-> "OE2" Residue "G GLU 527": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 27362 Number of models: 1 Model: "" Number of chains: 20 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 910 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "I" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 910 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "J" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 910 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 870 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "L" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 870 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 870 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "B" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "C" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 374} Chain breaks: 2 Chain: "D" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "E" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "F" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "G" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.57, per 1000 atoms: 0.50 Number of scatterers: 27362 At special positions: 0 Unit cell: (161.04, 165, 121.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 199 16.00 P 21 15.00 Mg 7 11.99 O 5181 8.00 N 4579 7.00 C 17375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.33 Conformation dependent library (CDL) restraints added in 4.2 seconds 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6530 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 10 sheets defined 50.6% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'H' and resid 4 through 17 removed outlier: 3.629A pdb=" N LEU H 10 " --> pdb=" O GLU H 6 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR H 15 " --> pdb=" O SER H 11 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG H 16 " --> pdb=" O THR H 12 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 32 removed outlier: 4.419A pdb=" N THR H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 50 through 64 removed outlier: 3.834A pdb=" N ARG H 63 " --> pdb=" O ARG H 59 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN H 64 " --> pdb=" O ILE H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 75 No H-bonds generated for 'chain 'H' and resid 72 through 75' Processing helix chain 'H' and resid 81 through 95 removed outlier: 3.881A pdb=" N PHE H 86 " --> pdb=" O HIS H 82 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA H 94 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE H 95 " --> pdb=" O ILE H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 104 Processing helix chain 'H' and resid 107 through 109 No H-bonds generated for 'chain 'H' and resid 107 through 109' Processing helix chain 'I' and resid 4 through 17 removed outlier: 3.629A pdb=" N LEU I 10 " --> pdb=" O GLU I 6 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N HIS I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR I 15 " --> pdb=" O SER I 11 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG I 16 " --> pdb=" O THR I 12 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 32 removed outlier: 4.418A pdb=" N THR I 28 " --> pdb=" O ARG I 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 50 through 64 removed outlier: 3.833A pdb=" N ARG I 63 " --> pdb=" O ARG I 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN I 64 " --> pdb=" O ILE I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 75 No H-bonds generated for 'chain 'I' and resid 72 through 75' Processing helix chain 'I' and resid 81 through 95 removed outlier: 3.881A pdb=" N PHE I 86 " --> pdb=" O HIS I 82 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA I 94 " --> pdb=" O TYR I 90 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE I 95 " --> pdb=" O ILE I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 104 Processing helix chain 'I' and resid 107 through 109 No H-bonds generated for 'chain 'I' and resid 107 through 109' Processing helix chain 'J' and resid 4 through 17 removed outlier: 3.629A pdb=" N LEU J 10 " --> pdb=" O GLU J 6 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS J 14 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR J 15 " --> pdb=" O SER J 11 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG J 16 " --> pdb=" O THR J 12 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 32 removed outlier: 4.418A pdb=" N THR J 28 " --> pdb=" O ARG J 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 50 through 64 removed outlier: 3.832A pdb=" N ARG J 63 " --> pdb=" O ARG J 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 75 No H-bonds generated for 'chain 'J' and resid 72 through 75' Processing helix chain 'J' and resid 81 through 95 removed outlier: 3.881A pdb=" N PHE J 86 " --> pdb=" O HIS J 82 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA J 94 " --> pdb=" O TYR J 90 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE J 95 " --> pdb=" O ILE J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 104 Processing helix chain 'J' and resid 107 through 109 No H-bonds generated for 'chain 'J' and resid 107 through 109' Processing helix chain 'K' and resid 4 through 17 removed outlier: 3.631A pdb=" N LEU K 10 " --> pdb=" O GLU K 6 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS K 14 " --> pdb=" O LEU K 10 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N THR K 15 " --> pdb=" O SER K 11 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG K 16 " --> pdb=" O THR K 12 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 32 removed outlier: 4.378A pdb=" N THR K 28 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 50 through 64 removed outlier: 3.542A pdb=" N ARG K 62 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG K 63 " --> pdb=" O ARG K 59 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN K 64 " --> pdb=" O ILE K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 75 No H-bonds generated for 'chain 'K' and resid 72 through 75' Processing helix chain 'K' and resid 81 through 95 removed outlier: 3.836A pdb=" N PHE K 86 " --> pdb=" O HIS K 82 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA K 94 " --> pdb=" O TYR K 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 17 removed outlier: 3.629A pdb=" N LEU L 10 " --> pdb=" O GLU L 6 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS L 14 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N THR L 15 " --> pdb=" O SER L 11 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG L 16 " --> pdb=" O THR L 12 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 32 removed outlier: 4.377A pdb=" N THR L 28 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 45 Processing helix chain 'L' and resid 50 through 64 removed outlier: 3.542A pdb=" N ARG L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG L 63 " --> pdb=" O ARG L 59 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN L 64 " --> pdb=" O ILE L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 75 No H-bonds generated for 'chain 'L' and resid 72 through 75' Processing helix chain 'L' and resid 81 through 95 removed outlier: 3.836A pdb=" N PHE L 86 " --> pdb=" O HIS L 82 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA L 94 " --> pdb=" O TYR L 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 17 removed outlier: 3.629A pdb=" N LEU M 10 " --> pdb=" O GLU M 6 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS M 14 " --> pdb=" O LEU M 10 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N THR M 15 " --> pdb=" O SER M 11 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG M 16 " --> pdb=" O THR M 12 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 32 removed outlier: 4.377A pdb=" N THR M 28 " --> pdb=" O ARG M 24 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR M 29 " --> pdb=" O ASP M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 45 Processing helix chain 'M' and resid 50 through 63 removed outlier: 3.543A pdb=" N ARG M 62 " --> pdb=" O LEU M 58 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG M 63 " --> pdb=" O ARG M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 75 No H-bonds generated for 'chain 'M' and resid 72 through 75' Processing helix chain 'M' and resid 81 through 95 removed outlier: 3.836A pdb=" N PHE M 86 " --> pdb=" O HIS M 82 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA M 94 " --> pdb=" O TYR M 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.809A pdb=" N LYS A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 172 Processing helix chain 'A' and resid 199 through 211 removed outlier: 4.271A pdb=" N PHE A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 238 removed outlier: 3.509A pdb=" N ALA A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 263 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.538A pdb=" N TYR A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 326 removed outlier: 3.698A pdb=" N LYS A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 Processing helix chain 'A' and resid 345 through 363 removed outlier: 3.567A pdb=" N LEU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N LEU A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 removed outlier: 4.419A pdb=" N ARG A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 removed outlier: 3.653A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 411 No H-bonds generated for 'chain 'A' and resid 408 through 411' Processing helix chain 'A' and resid 429 through 439 Processing helix chain 'A' and resid 458 through 465 removed outlier: 4.193A pdb=" N LEU A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 485 removed outlier: 3.812A pdb=" N ALA A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 540 No H-bonds generated for 'chain 'A' and resid 537 through 540' Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 134 through 147 removed outlier: 3.808A pdb=" N LYS B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 143 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 144 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.516A pdb=" N SER B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 removed outlier: 4.270A pdb=" N PHE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 211 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 241 removed outlier: 3.511A pdb=" N ALA B 238 " --> pdb=" O MET B 234 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE B 240 " --> pdb=" O CYS B 236 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 263 Processing helix chain 'B' and resid 295 through 305 removed outlier: 3.537A pdb=" N TYR B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'B' and resid 330 through 340 removed outlier: 3.610A pdb=" N CYS B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 356 removed outlier: 3.549A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 354 " --> pdb=" O GLN B 350 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 4.302A pdb=" N VAL B 363 " --> pdb=" O GLY B 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 359 through 363' Processing helix chain 'B' and resid 375 through 383 removed outlier: 4.420A pdb=" N ARG B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 396 removed outlier: 3.657A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 Processing helix chain 'B' and resid 427 through 439 removed outlier: 3.565A pdb=" N LYS B 435 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 437 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 467 removed outlier: 3.954A pdb=" N LEU B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 486 removed outlier: 4.005A pdb=" N GLU B 481 " --> pdb=" O ILE B 477 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 541 removed outlier: 5.072A pdb=" N LYS B 538 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B 541 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 134 through 145 removed outlier: 3.809A pdb=" N LYS C 142 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS C 143 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 144 " --> pdb=" O VAL C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 172 Processing helix chain 'C' and resid 199 through 211 removed outlier: 4.270A pdb=" N PHE C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 211 " --> pdb=" O ILE C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 241 removed outlier: 3.511A pdb=" N ALA C 238 " --> pdb=" O MET C 234 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE C 240 " --> pdb=" O CYS C 236 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP C 241 " --> pdb=" O ASN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 263 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 295 through 305 removed outlier: 3.538A pdb=" N TYR C 299 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP C 300 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 325 removed outlier: 3.935A pdb=" N LYS C 321 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 340 Processing helix chain 'C' and resid 345 through 363 removed outlier: 3.570A pdb=" N LEU C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 363 " --> pdb=" O GLY C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 383 removed outlier: 4.420A pdb=" N ARG C 380 " --> pdb=" O MET C 376 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 398 removed outlier: 3.663A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 392 " --> pdb=" O GLU C 388 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 428 through 439 removed outlier: 3.564A pdb=" N LYS C 435 " --> pdb=" O ASP C 432 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU C 437 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 465 removed outlier: 4.147A pdb=" N LEU C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 484 removed outlier: 3.812A pdb=" N ALA C 474 " --> pdb=" O ALA C 470 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 540 No H-bonds generated for 'chain 'C' and resid 537 through 540' Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 134 through 145 removed outlier: 3.810A pdb=" N LYS D 142 " --> pdb=" O ASP D 138 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 143 " --> pdb=" O ARG D 139 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 144 " --> pdb=" O VAL D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 172 Processing helix chain 'D' and resid 199 through 211 removed outlier: 4.271A pdb=" N PHE D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET D 210 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 211 " --> pdb=" O ILE D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 228 through 238 removed outlier: 3.511A pdb=" N ALA D 238 " --> pdb=" O MET D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 263 Processing helix chain 'D' and resid 295 through 305 removed outlier: 3.537A pdb=" N TYR D 299 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP D 300 " --> pdb=" O ASP D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 325 removed outlier: 3.789A pdb=" N LYS D 321 " --> pdb=" O ASP D 317 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 337 Processing helix chain 'D' and resid 345 through 356 removed outlier: 4.086A pdb=" N GLN D 350 " --> pdb=" O GLU D 346 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU D 356 " --> pdb=" O ASN D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 363 removed outlier: 4.306A pdb=" N VAL D 363 " --> pdb=" O GLY D 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 359 through 363' Processing helix chain 'D' and resid 374 through 383 removed outlier: 4.420A pdb=" N ARG D 380 " --> pdb=" O MET D 376 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 395 removed outlier: 3.665A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 392 " --> pdb=" O GLU D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 411 Processing helix chain 'D' and resid 425 through 439 removed outlier: 4.054A pdb=" N ASP D 428 " --> pdb=" O GLN D 425 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS D 435 " --> pdb=" O ASP D 432 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU D 437 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 465 removed outlier: 4.170A pdb=" N LEU D 464 " --> pdb=" O ILE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 485 removed outlier: 3.814A pdb=" N ALA D 474 " --> pdb=" O ALA D 470 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU D 481 " --> pdb=" O ILE D 477 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN D 482 " --> pdb=" O SER D 478 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 540 removed outlier: 5.562A pdb=" N LYS D 538 " --> pdb=" O LEU D 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 121 Processing helix chain 'E' and resid 134 through 145 removed outlier: 3.809A pdb=" N LYS E 142 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS E 143 " --> pdb=" O ARG E 139 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 175 removed outlier: 3.639A pdb=" N SER E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 211 removed outlier: 4.271A pdb=" N PHE E 204 " --> pdb=" O THR E 200 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET E 210 " --> pdb=" O ASP E 206 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E 211 " --> pdb=" O ILE E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 241 removed outlier: 3.511A pdb=" N ALA E 238 " --> pdb=" O MET E 234 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE E 240 " --> pdb=" O CYS E 236 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP E 241 " --> pdb=" O ASN E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 263 Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 295 through 305 removed outlier: 3.536A pdb=" N TYR E 299 " --> pdb=" O ILE E 295 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP E 300 " --> pdb=" O ASP E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 325 removed outlier: 3.960A pdb=" N LYS E 321 " --> pdb=" O ASP E 317 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR E 322 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE E 323 " --> pdb=" O LEU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 334 Processing helix chain 'E' and resid 345 through 363 removed outlier: 4.146A pdb=" N GLN E 350 " --> pdb=" O GLU E 346 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN E 353 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU E 360 " --> pdb=" O GLU E 356 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL E 361 " --> pdb=" O SER E 357 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY E 362 " --> pdb=" O ARG E 358 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL E 363 " --> pdb=" O GLY E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 383 removed outlier: 4.419A pdb=" N ARG E 380 " --> pdb=" O MET E 376 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 397 removed outlier: 3.666A pdb=" N SER E 391 " --> pdb=" O ASP E 387 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA E 392 " --> pdb=" O GLU E 388 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 411 Processing helix chain 'E' and resid 425 through 427 No H-bonds generated for 'chain 'E' and resid 425 through 427' Processing helix chain 'E' and resid 429 through 439 Processing helix chain 'E' and resid 458 through 467 Processing helix chain 'E' and resid 470 through 484 removed outlier: 4.275A pdb=" N ALA E 474 " --> pdb=" O ALA E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'F' and resid 114 through 121 Processing helix chain 'F' and resid 137 through 147 removed outlier: 3.809A pdb=" N LYS F 142 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS F 143 " --> pdb=" O ARG F 139 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU F 144 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET F 147 " --> pdb=" O LYS F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 172 Processing helix chain 'F' and resid 199 through 211 removed outlier: 4.270A pdb=" N PHE F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET F 210 " --> pdb=" O ASP F 206 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU F 211 " --> pdb=" O ILE F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 241 removed outlier: 3.508A pdb=" N ALA F 238 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE F 240 " --> pdb=" O CYS F 236 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASP F 241 " --> pdb=" O ASN F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 264 Processing helix chain 'F' and resid 276 through 280 Processing helix chain 'F' and resid 295 through 304 removed outlier: 3.536A pdb=" N TYR F 299 " --> pdb=" O ILE F 295 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP F 300 " --> pdb=" O ASP F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 326 removed outlier: 3.811A pdb=" N ASN F 320 " --> pdb=" O GLU F 316 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS F 321 " --> pdb=" O ASP F 317 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE F 323 " --> pdb=" O LEU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 339 Processing helix chain 'F' and resid 345 through 363 removed outlier: 8.820A pdb=" N LEU F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL F 361 " --> pdb=" O SER F 357 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL F 363 " --> pdb=" O GLY F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 383 removed outlier: 4.419A pdb=" N ARG F 380 " --> pdb=" O MET F 376 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 394 removed outlier: 3.665A pdb=" N SER F 391 " --> pdb=" O ASP F 387 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA F 392 " --> pdb=" O GLU F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 412 removed outlier: 3.586A pdb=" N CYS F 412 " --> pdb=" O LYS F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 439 removed outlier: 3.946A pdb=" N LEU F 437 " --> pdb=" O LEU F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 467 Processing helix chain 'F' and resid 470 through 482 removed outlier: 3.961A pdb=" N ALA F 474 " --> pdb=" O ALA F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'G' and resid 114 through 121 Processing helix chain 'G' and resid 134 through 145 removed outlier: 3.810A pdb=" N LYS G 142 " --> pdb=" O ASP G 138 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS G 143 " --> pdb=" O ARG G 139 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 172 Processing helix chain 'G' and resid 199 through 211 removed outlier: 4.271A pdb=" N PHE G 204 " --> pdb=" O THR G 200 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET G 210 " --> pdb=" O ASP G 206 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU G 211 " --> pdb=" O ILE G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 225 No H-bonds generated for 'chain 'G' and resid 223 through 225' Processing helix chain 'G' and resid 228 through 238 removed outlier: 3.511A pdb=" N ALA G 238 " --> pdb=" O MET G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 263 Processing helix chain 'G' and resid 276 through 280 Processing helix chain 'G' and resid 295 through 305 removed outlier: 3.537A pdb=" N TYR G 299 " --> pdb=" O ILE G 295 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP G 300 " --> pdb=" O ASP G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 326 removed outlier: 3.696A pdb=" N LYS G 321 " --> pdb=" O ASP G 317 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR G 322 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE G 323 " --> pdb=" O LEU G 319 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER G 326 " --> pdb=" O THR G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 339 removed outlier: 3.641A pdb=" N PHE G 336 " --> pdb=" O THR G 332 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER G 339 " --> pdb=" O MET G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 355 Processing helix chain 'G' and resid 360 through 363 No H-bonds generated for 'chain 'G' and resid 360 through 363' Processing helix chain 'G' and resid 374 through 383 removed outlier: 4.420A pdb=" N ARG G 380 " --> pdb=" O MET G 376 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS G 381 " --> pdb=" O ALA G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 394 Processing helix chain 'G' and resid 407 through 411 Processing helix chain 'G' and resid 427 through 442 removed outlier: 3.565A pdb=" N LYS G 435 " --> pdb=" O ASP G 432 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU G 437 " --> pdb=" O LEU G 434 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG G 440 " --> pdb=" O LEU G 437 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLY G 441 " --> pdb=" O SER G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 467 removed outlier: 4.262A pdb=" N LEU G 464 " --> pdb=" O ILE G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 485 Processing helix chain 'G' and resid 534 through 542 removed outlier: 5.540A pdb=" N LYS G 538 " --> pdb=" O LEU G 535 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP G 541 " --> pdb=" O LYS G 538 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 285 through 290 removed outlier: 6.481A pdb=" N PHE A 154 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE A 288 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE A 156 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 290 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N HIS A 158 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N CYS A 268 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU A 157 " --> pdb=" O CYS A 268 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 270 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLY A 159 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR A 272 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 444 through 447 Processing sheet with id= C, first strand: chain 'B' and resid 285 through 290 removed outlier: 6.456A pdb=" N PHE B 154 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE B 288 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE B 156 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 290 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N HIS B 158 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N CYS B 268 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU B 157 " --> pdb=" O CYS B 268 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 270 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLY B 159 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR B 272 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU B 269 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE B 247 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR B 271 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE B 249 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER B 186 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL B 248 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 188 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP B 250 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 190 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B 252 " --> pdb=" O LEU B 190 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'C' and resid 285 through 287 removed outlier: 6.482A pdb=" N PHE C 154 " --> pdb=" O GLU C 286 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N CYS C 268 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU C 157 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL C 270 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU C 269 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE C 247 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR C 271 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE C 249 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER C 186 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL C 248 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C 188 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASP C 250 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU C 190 " --> pdb=" O ASP C 250 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL C 252 " --> pdb=" O LEU C 190 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'D' and resid 285 through 290 removed outlier: 6.481A pdb=" N PHE D 154 " --> pdb=" O GLU D 286 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE D 288 " --> pdb=" O PHE D 154 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE D 156 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL D 290 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N HIS D 158 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N CYS D 268 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU D 157 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL D 270 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLY D 159 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR D 272 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LEU D 269 " --> pdb=" O THR D 245 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE D 247 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N THR D 271 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE D 249 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER D 186 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL D 248 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL D 188 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP D 250 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU D 190 " --> pdb=" O ASP D 250 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL D 252 " --> pdb=" O LEU D 190 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'E' and resid 285 through 290 removed outlier: 6.481A pdb=" N PHE E 154 " --> pdb=" O GLU E 286 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE E 288 " --> pdb=" O PHE E 154 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE E 156 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL E 290 " --> pdb=" O PHE E 156 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N HIS E 158 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N CYS E 268 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU E 157 " --> pdb=" O CYS E 268 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL E 270 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY E 159 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N THR E 272 " --> pdb=" O GLY E 159 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU E 269 " --> pdb=" O THR E 245 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE E 247 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR E 271 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE E 249 " --> pdb=" O THR E 271 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER E 186 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL E 248 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL E 188 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASP E 250 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU E 190 " --> pdb=" O ASP E 250 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL E 252 " --> pdb=" O LEU E 190 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'E' and resid 445 through 447 Processing sheet with id= H, first strand: chain 'F' and resid 284 through 287 removed outlier: 6.875A pdb=" N CYS F 268 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER F 186 " --> pdb=" O LEU F 246 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL F 248 " --> pdb=" O SER F 186 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL F 188 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASP F 250 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU F 190 " --> pdb=" O ASP F 250 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL F 252 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 445 through 447 Processing sheet with id= J, first strand: chain 'G' and resid 285 through 287 removed outlier: 6.659A pdb=" N PHE G 154 " --> pdb=" O GLU G 286 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N CYS G 268 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE G 247 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N THR G 271 " --> pdb=" O PHE G 247 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE G 249 " --> pdb=" O THR G 271 " (cutoff:3.500A) 804 hydrogen bonds defined for protein. 2226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.18 Time building geometry restraints manager: 12.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7938 1.33 - 1.46: 5781 1.46 - 1.59: 13798 1.59 - 1.72: 21 1.72 - 1.85: 316 Bond restraints: 27854 Sorted by residual: bond pdb=" C4 ATP E 602 " pdb=" C5 ATP E 602 " ideal model delta sigma weight residual 1.388 1.484 -0.096 1.00e-02 1.00e+04 9.31e+01 bond pdb=" C4 ATP G 602 " pdb=" C5 ATP G 602 " ideal model delta sigma weight residual 1.388 1.484 -0.096 1.00e-02 1.00e+04 9.24e+01 bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.484 -0.096 1.00e-02 1.00e+04 9.13e+01 bond pdb=" C4 ATP C 602 " pdb=" C5 ATP C 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 9.10e+01 bond pdb=" C4 ATP A 602 " pdb=" C5 ATP A 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 9.04e+01 ... (remaining 27849 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.47: 529 104.47 - 112.15: 13258 112.15 - 119.83: 10976 119.83 - 127.51: 12743 127.51 - 135.19: 170 Bond angle restraints: 37676 Sorted by residual: angle pdb=" PB ATP E 602 " pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " ideal model delta sigma weight residual 139.87 114.14 25.73 1.00e+00 1.00e+00 6.62e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 114.18 25.69 1.00e+00 1.00e+00 6.60e+02 angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 114.20 25.67 1.00e+00 1.00e+00 6.59e+02 angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 114.21 25.66 1.00e+00 1.00e+00 6.58e+02 angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 114.23 25.64 1.00e+00 1.00e+00 6.57e+02 ... (remaining 37671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.73: 15106 25.73 - 51.46: 1469 51.46 - 77.20: 408 77.20 - 102.93: 32 102.93 - 128.66: 6 Dihedral angle restraints: 17021 sinusoidal: 7056 harmonic: 9965 Sorted by residual: dihedral pdb=" CA MET A 449 " pdb=" C MET A 449 " pdb=" N PRO A 450 " pdb=" CA PRO A 450 " ideal model delta harmonic sigma weight residual -180.00 -51.34 -128.66 0 5.00e+00 4.00e-02 6.62e+02 dihedral pdb=" CA MET G 449 " pdb=" C MET G 449 " pdb=" N PRO G 450 " pdb=" CA PRO G 450 " ideal model delta harmonic sigma weight residual -180.00 -51.39 -128.61 0 5.00e+00 4.00e-02 6.62e+02 dihedral pdb=" CA MET B 449 " pdb=" C MET B 449 " pdb=" N PRO B 450 " pdb=" CA PRO B 450 " ideal model delta harmonic sigma weight residual -180.00 -51.40 -128.60 0 5.00e+00 4.00e-02 6.61e+02 ... (remaining 17018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2916 0.070 - 0.139: 1088 0.139 - 0.209: 263 0.209 - 0.279: 58 0.279 - 0.348: 12 Chirality restraints: 4337 Sorted by residual: chirality pdb=" CA PHE E 204 " pdb=" N PHE E 204 " pdb=" C PHE E 204 " pdb=" CB PHE E 204 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA PHE C 532 " pdb=" N PHE C 532 " pdb=" C PHE C 532 " pdb=" CB PHE C 532 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA PHE A 532 " pdb=" N PHE A 532 " pdb=" C PHE A 532 " pdb=" CB PHE A 532 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 4334 not shown) Planarity restraints: 4780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 443 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.24e+01 pdb=" C LEU B 443 " -0.061 2.00e-02 2.50e+03 pdb=" O LEU B 443 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU B 444 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 148 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C CYS C 148 " -0.061 2.00e-02 2.50e+03 pdb=" O CYS C 148 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP C 149 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 336 " 0.016 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C PHE E 336 " -0.059 2.00e-02 2.50e+03 pdb=" O PHE E 336 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE E 337 " 0.019 2.00e-02 2.50e+03 ... (remaining 4777 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 151 2.43 - 3.05: 20259 3.05 - 3.67: 42056 3.67 - 4.28: 64789 4.28 - 4.90: 99332 Nonbonded interactions: 226587 Sorted by model distance: nonbonded pdb=" OG1 THR A 367 " pdb=" CD PRO A 368 " model vdw 1.813 3.440 nonbonded pdb=" CD PRO A 530 " pdb=" NZ LYS A 531 " model vdw 1.994 3.520 nonbonded pdb=" CD PRO B 530 " pdb=" NZ LYS B 531 " model vdw 1.995 3.520 nonbonded pdb=" CD PRO E 530 " pdb=" NZ LYS E 531 " model vdw 1.995 3.520 nonbonded pdb=" CD PRO C 530 " pdb=" NZ LYS C 531 " model vdw 1.995 3.520 ... (remaining 226582 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = (chain 'H' and resid 1 through 105) selection = (chain 'I' and resid 1 through 105) selection = (chain 'J' and resid 1 through 105) selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.220 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 68.460 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.096 27854 Z= 0.601 Angle : 1.485 25.727 37676 Z= 1.071 Chirality : 0.076 0.348 4337 Planarity : 0.006 0.059 4780 Dihedral : 20.623 128.660 10491 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 62.06 Ramachandran Plot: Outliers : 1.32 % Allowed : 13.79 % Favored : 84.89 % Rotamer Outliers : 27.27 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.82 (0.12), residues: 3328 helix: -3.40 (0.09), residues: 1803 sheet: -1.88 (0.31), residues: 259 loop : -2.89 (0.16), residues: 1266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1169 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 840 poor density : 329 time to evaluate : 3.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 840 outliers final: 210 residues processed: 1066 average time/residue: 0.4172 time to fit residues: 683.6183 Evaluate side-chains 438 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 228 time to evaluate : 3.289 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 210 outliers final: 3 residues processed: 210 average time/residue: 0.2885 time to fit residues: 110.8932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 171 optimal weight: 0.6980 chunk 136 optimal weight: 6.9990 chunk 263 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 305 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 34 ASN I 34 ASN I 56 ASN J 34 ASN J 56 ASN K 34 ASN L 34 ASN M 34 ASN M 64 GLN A 123 ASN A 237 ASN A 244 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN A 283 GLN A 471 GLN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 244 ASN B 471 GLN B 482 GLN C 123 ASN ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 ASN C 471 GLN C 482 GLN C 537 GLN D 123 ASN D 225 HIS ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN D 283 GLN D 471 GLN D 537 GLN E 123 ASN E 237 ASN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 350 GLN E 471 GLN E 482 GLN F 123 ASN ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 ASN F 244 ASN F 262 GLN F 329 ASN F 352 ASN F 471 GLN ** F 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN ** G 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 ASN G 283 GLN ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 GLN G 458 HIS G 466 HIS G 471 GLN G 475 ASN G 482 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 27854 Z= 0.276 Angle : 0.805 11.163 37676 Z= 0.403 Chirality : 0.044 0.208 4337 Planarity : 0.007 0.104 4780 Dihedral : 6.883 78.073 3650 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.44 % Favored : 94.11 % Rotamer Outliers : 4.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.13), residues: 3328 helix: -2.03 (0.11), residues: 1746 sheet: -0.87 (0.30), residues: 259 loop : -2.06 (0.16), residues: 1323 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 250 time to evaluate : 3.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 138 outliers final: 47 residues processed: 369 average time/residue: 0.3729 time to fit residues: 220.5963 Evaluate side-chains 240 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 193 time to evaluate : 3.329 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.2382 time to fit residues: 25.4661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 305 optimal weight: 0.0030 chunk 330 optimal weight: 7.9990 chunk 272 optimal weight: 3.9990 chunk 303 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 245 optimal weight: 9.9990 overall best weight: 2.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN ** A 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN B 123 ASN B 283 GLN C 237 ASN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN ** C 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 ASN ** F 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 GLN G 237 ASN ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 27854 Z= 0.239 Angle : 0.710 20.062 37676 Z= 0.347 Chirality : 0.041 0.185 4337 Planarity : 0.006 0.064 4780 Dihedral : 6.651 74.711 3650 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.38 % Favored : 94.32 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3328 helix: -0.88 (0.12), residues: 1772 sheet: -0.57 (0.30), residues: 259 loop : -1.43 (0.17), residues: 1297 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 205 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 29 residues processed: 280 average time/residue: 0.3882 time to fit residues: 174.8724 Evaluate side-chains 212 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 183 time to evaluate : 3.509 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2537 time to fit residues: 18.1714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 33 optimal weight: 60.0000 chunk 145 optimal weight: 1.9990 chunk 205 optimal weight: 0.0970 chunk 306 optimal weight: 0.7980 chunk 324 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 290 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 HIS D 237 ASN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 ASN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 534 GLN ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 HIS G 254 GLN ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.5808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 27854 Z= 0.177 Angle : 0.654 15.119 37676 Z= 0.315 Chirality : 0.039 0.176 4337 Planarity : 0.006 0.065 4780 Dihedral : 6.445 72.709 3650 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.63 % Favored : 95.19 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.15), residues: 3328 helix: -0.29 (0.12), residues: 1785 sheet: -0.33 (0.30), residues: 259 loop : -1.20 (0.18), residues: 1284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 210 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 26 residues processed: 264 average time/residue: 0.3778 time to fit residues: 161.2143 Evaluate side-chains 219 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 3.272 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2960 time to fit residues: 17.7131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 1.9990 chunk 184 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 241 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 277 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 165 optimal weight: 3.9990 chunk 291 optimal weight: 5.9990 chunk 81 optimal weight: 0.0970 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 40 HIS J 56 ASN ** A 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 HIS ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 GLN ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 536 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.6348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 27854 Z= 0.238 Angle : 0.665 13.763 37676 Z= 0.322 Chirality : 0.039 0.220 4337 Planarity : 0.006 0.064 4780 Dihedral : 6.396 76.586 3650 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.56 % Favored : 94.41 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3328 helix: 0.00 (0.13), residues: 1770 sheet: -0.15 (0.31), residues: 259 loop : -0.94 (0.18), residues: 1299 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 200 time to evaluate : 3.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 17 residues processed: 246 average time/residue: 0.4049 time to fit residues: 159.5533 Evaluate side-chains 203 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 186 time to evaluate : 3.113 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2390 time to fit residues: 12.0132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 7.9990 chunk 292 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 190 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 325 optimal weight: 7.9990 chunk 269 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 ASN I 64 GLN ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 HIS ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 ASN ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 482 GLN F 534 GLN ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.6916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 27854 Z= 0.313 Angle : 0.709 12.668 37676 Z= 0.342 Chirality : 0.040 0.194 4337 Planarity : 0.005 0.062 4780 Dihedral : 6.448 76.662 3650 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.71 % Favored : 94.26 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3328 helix: 0.12 (0.13), residues: 1728 sheet: 0.11 (0.33), residues: 259 loop : -0.80 (0.18), residues: 1341 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 189 time to evaluate : 3.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 25 residues processed: 236 average time/residue: 0.3839 time to fit residues: 147.3562 Evaluate side-chains 202 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 3.479 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2598 time to fit residues: 16.7253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 9.9990 chunk 36 optimal weight: 40.0000 chunk 185 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 273 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 323 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 ASN A 534 GLN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.7368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 27854 Z= 0.327 Angle : 0.735 13.173 37676 Z= 0.352 Chirality : 0.041 0.179 4337 Planarity : 0.005 0.062 4780 Dihedral : 6.418 76.752 3650 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.98 % Favored : 93.96 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3328 helix: -0.02 (0.13), residues: 1783 sheet: 0.24 (0.33), residues: 259 loop : -1.01 (0.18), residues: 1286 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 190 time to evaluate : 3.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 21 residues processed: 231 average time/residue: 0.3815 time to fit residues: 143.6764 Evaluate side-chains 205 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 184 time to evaluate : 3.289 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2460 time to fit residues: 14.1216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.7521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 27854 Z= 0.181 Angle : 0.698 13.308 37676 Z= 0.327 Chirality : 0.040 0.201 4337 Planarity : 0.005 0.063 4780 Dihedral : 6.305 75.227 3650 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.77 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3328 helix: 0.32 (0.13), residues: 1780 sheet: 0.26 (0.33), residues: 259 loop : -0.84 (0.19), residues: 1289 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 194 time to evaluate : 3.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 202 average time/residue: 0.3757 time to fit residues: 124.9898 Evaluate side-chains 186 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 181 time to evaluate : 4.143 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2614 time to fit residues: 7.0581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 3.9990 chunk 310 optimal weight: 0.8980 chunk 283 optimal weight: 1.9990 chunk 301 optimal weight: 7.9990 chunk 181 optimal weight: 0.1980 chunk 131 optimal weight: 1.9990 chunk 236 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 285 optimal weight: 0.7980 chunk 300 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 56 ASN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.7702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 27854 Z= 0.175 Angle : 0.718 15.274 37676 Z= 0.331 Chirality : 0.040 0.205 4337 Planarity : 0.005 0.064 4780 Dihedral : 6.177 78.742 3650 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.99 % Favored : 94.98 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 3328 helix: 0.58 (0.13), residues: 1731 sheet: 0.34 (0.33), residues: 259 loop : -0.75 (0.18), residues: 1338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 193 time to evaluate : 3.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 201 average time/residue: 0.3800 time to fit residues: 124.7918 Evaluate side-chains 184 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 3.384 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2634 time to fit residues: 6.0578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 5.9990 chunk 319 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 334 optimal weight: 0.9990 chunk 308 optimal weight: 0.4980 chunk 266 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 205 optimal weight: 0.2980 chunk 163 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN L 56 ASN A 225 HIS ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 ASN ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.7839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 27854 Z= 0.175 Angle : 0.715 14.552 37676 Z= 0.329 Chirality : 0.040 0.195 4337 Planarity : 0.005 0.064 4780 Dihedral : 6.077 79.958 3650 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 3328 helix: 0.58 (0.13), residues: 1742 sheet: 0.43 (0.33), residues: 259 loop : -0.72 (0.18), residues: 1327 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 188 time to evaluate : 3.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 193 average time/residue: 0.3900 time to fit residues: 123.0873 Evaluate side-chains 187 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 184 time to evaluate : 3.522 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2899 time to fit residues: 6.1989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 1.9990 chunk 283 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 245 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 74 optimal weight: 0.0570 chunk 266 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 274 optimal weight: 8.9990 chunk 33 optimal weight: 50.0000 chunk 49 optimal weight: 20.0000 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.086642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.053765 restraints weight = 198460.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.050996 restraints weight = 152526.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.051102 restraints weight = 115688.032| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.7962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 27854 Z= 0.181 Angle : 0.724 12.574 37676 Z= 0.333 Chirality : 0.040 0.256 4337 Planarity : 0.005 0.061 4780 Dihedral : 6.035 80.717 3650 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.75 % Favored : 95.19 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3328 helix: 0.57 (0.13), residues: 1742 sheet: 0.52 (0.33), residues: 259 loop : -0.60 (0.19), residues: 1327 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5392.48 seconds wall clock time: 99 minutes 34.50 seconds (5974.50 seconds total)